tblastn

Quick Start

• Command: tblastn -query <protein.fa> -db <nucl_db> -out <results.txt>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/tblastn
• Version: 2.17.0+
• Full reference: See references/help.md for complete option documentation

When To Use This Tool

• Search protein queries against nucleotide databases translated in six frames.
• Find coding regions or protein homologs in genomes, contigs, or transcript assemblies.
• Use this when protein-level sensitivity is useful but the target is still nucleotide.
• Prefer blastp when both query and target are already protein.

Common Patterns

# 1) Search proteins against a nucleotide database
tblastn \
  -query proteins.fa \
  -db transcripts_db \
  -outfmt "6 qaccver saccver pident length evalue bitscore" \
  -evalue 1e-5 \
  -max_target_seqs 20 \
  -num_threads 8

# 2) Use an alternative genetic code
tblastn \
  -query proteins.fa \
  -db bacterial_db \
  -db_gencode 11 \
  -outfmt 6

# 3) Allow gapped translated hits across longer introns
tblastn \
  -query proteins.fa \
  -db genome_db \
  -max_intron_length 10000 \
  -outfmt 7

Recommended Workflow

1. Build or select a nucleotide BLAST database first.
2. Choose the correct translation table with -db_gencode if the organism is non-standard.
3. Emit tabular output unless manual pairwise inspection is explicitly needed.
4. Confirm top hits make biological sense before inferring annotation from translated matches.

Guardrails

• The database or subject must be nucleotide, not protein.
• -db_gencode affects translation, so set it explicitly for mitochondrial or non-standard codes.
• -max_intron_length matters when searching genomic targets with interrupted coding sequence.
• For anything larger than a toy example, pre-format the target with makeblastdb instead of using -subject.